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Bacterial promoter modelling and prediction for E. coli and B. subtilis with Beagle

Maetschke, Stefan R., Towsey, Michael W., & Hogan, James M. (2006) Bacterial promoter modelling and prediction for E. coli and B. subtilis with Beagle. In Workshop on Intelligent Systems for Bioinformatics (WISB-2006), 4th December 2006, Hobart, Tasmania.

Abstract

We constructed sigma70-promoter models of varying complexity to predict promoter locations and to evaluate the importance of specific promoter elements. For this purpose, a novel software, named Beagle, was developed that utilizes an easy description language to conveniently specify promoter models. Model specifications are translated into position weight matrices and gap distributions which are refined using data from known promoters. The method is transparent, fast and allows the rapid exploration of different promoter models. Applied to promoter prediction in E. coli and B. subtilis, we show that inclusion of UP-elements and extended -10 motifs into the model yields a significant increase in prediction accuracy. The software, data sets and extended results can be downloaded at http://eresearch.fit.qut.edu.au/Beagle/.

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ID Code: 7583
Item Type: Conference Paper
Additional URLs:
Keywords: Bacterial promoters, sigma factor, Escherichia coli, Bacillus subtilis
ISBN: 1920682546
ISSN: 1445-1336
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200) > Biological Mathematics (010202)
Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > ARTIFICIAL INTELLIGENCE AND IMAGE PROCESSING (080100) > Pattern Recognition and Data Mining (080109)
Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > ARTIFICIAL INTELLIGENCE AND IMAGE PROCESSING (080100) > Artificial Intelligence and Image Processing not elsewhere classified (080199)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2006 Australian Computer Society
Copyright Statement: Reproduced in accordance with the copyright policy of the publisher.
Deposited On: 14 May 2007
Last Modified: 29 Feb 2012 23:23

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